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Gene Card

Enter a TK1151 or OH-1004 gene ID to view sequences, annotations and analyses in the corresponding reference genome.
Flanking length, max 10000 bp
Examples TkA01G624900 LXL04_000258

Gene overview

TkA03G561890
Reference: TK1151 Chr: Chr03 Coordinates: 142624481-142628681 Strand: + Type: protein_coding

cDNA / CDS / Protein Sequences

Available sequence downloads CDS FASTA Protein FASTA cDNA FASTA

cDNA

Download cDNA FASTA

3301 bp · TkA03G561890|TK1151|cDNA

GCAAAAGGCGGTGCGGATTTTAAAGCCAAAACTTTGGGCAACAGTCATTTCAAAAGACCGGGAAAACAAAGGGCTTTCGGAGCGGAAACTTCAAGACACCAAATGGAGCATCAGTTATCATCGTGAAGTAAGCGAGAATAATCAGGTTCGTTTGCCATCTGGCACCTTCTTCGAATTGATATTGGAAAGGGGAAAAAGTTAGTCGATCTTCGTGTCTGCAGACTGCAATGGCATCTGTAAATGAGTCGGCTGCTTCTTCC...

CDS

Download CDS FASTA

2727 bp · TkA03G561890|TK1151|CDS

ATGGCATCTGTAAATGAGTCGGCTGCTTCTTCCTCCAAAACTAGGGTTCTTCCTTCATGGGGTTCTTCATCCGTGTCAAGTACTACAGGTTCCCGTGGATCAACTAAAAAGCCTCCTCCTTCTAAAAAGGAATCTACTTCAAACAGTCAAAAGTTGCCGACCAGTAAAGTTTATAAAAATTCAAGATGGTATACACTCACACATGGAAATCACAAGAAAGCTACTTTAAATCACGAATCTGATAACCAGATACCCCAGAA...

Protein

Download Protein FASTA

908 aa · TkA03G561890|TK1151|PROTEIN

MASVNESAASSSKTRVLPSWGSSSVSSTTGSRGSTKKPPPSKKESTSNSQKLPTSKVYKNSRWYTLTHGNHKKATLNHESDNQIPQKDTKRILSSYLQNSSSSNSNPTPQRNESYETNDLPASSSHTNFQPQDSFSFANNDVSMKNNNGRRLLPAFMNPHGSVSATQYAGQSGNSRPVVVQETVGDERLIYQVALRDLYQPTTEATLPEGLLSIPLFRHQKIALAWMLDKENSVACSGGILADDQGLGKTISVIALIQMQ...

Flanking Sequence Download

Sequence orientation and download details

Upstream/downstream are capped at 10000 bp per side. Negative-strand genes are reverse-complemented so the final FASTA follows transcriptional 5′→3′ orientation.

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ID Mapping

Input IDTkA03G561890
TK1151 IDTkA03G561890
OH-1004 IDLXL04_011047
Relationship / confidenceMulti Source To Oh1004 / Complex relationship
Protein identity (%)98.900
Protein coverage (%)TK1151 99.559 / OH-1004 61.875
Coverage and evidence

Coverage is the aligned span of the best-scoring HSP divided by representative protein length. A homolog match does not establish functional validation.

Source versionTK1151 / GWHBCHF00000000
Open Full ID Mapping
SNP / Indel variants and carrier samplesCRA009020 · TK1151

Expand to load variant records for this gene.

Basic Information and Functional Annotation

Gene IDTkA03G561890
LocationChr03:142624481-142628681 (+)
DescriptionSimilar to CHR28: Helicase-like transcription factor CHR28
Arabidopsis / Rice Reference Genes and Papers

Download references for this gene

Arabidopsis

Reference gene IDPossible functionPapers / DOI
At1g50410 Probable helicase-like transcription factor involved in transcriptional gene silencing.
SUVR2 is involved in transcriptional gene silencing by associating with SNF2-related chromatin-remodeling proteins in Arabidopsis.2014 · DOI: 10.1038/cr.2014.156
SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation.2014 · DOI: 10.1073/pnas.1420515111
At3g20010 Probable helicase-like transcription factor involved in transcriptional gene silencing.
SUVR2 is involved in transcriptional gene silencing by associating with SNF2-related chromatin-remodeling proteins in Arabidopsis.2014 · DOI: 10.1038/cr.2014.156
SNF2 chromatin remodeler-family proteins FRG1 and -2 are required for RNA-directed DNA methylation.2014 · DOI: 10.1073/pnas.1420515111
At5g43530 Possesses intrinsic ATP-dependent nucleosome-remodeling activity.
A homolog of ScRAD5 is involved in DNA repair and homologous recombination in Arabidopsis.2008 · DOI: 10.1104/pp.108.116806
At5g22750 Functions in error-free postreplication DNA repair or DNA- damage tolerance (DTT) pathway.
A homolog of ScRAD5 is involved in DNA repair and homologous recombination in Arabidopsis.2008 · DOI: 10.1104/pp.108.116806
RAD5A, RECQ4A, and MUS81 have specific functions in homologous recombination and define different pathways of DNA repair in Arabidopsis thaliana.2010 · DOI: 10.1105/tpc.110.078568
RAD5a and REV3 function in two alternative pathways of DNA-damage tolerance in Arabidopsis.2011 · DOI: 10.1016/j.dnarep.2011.04.009
AtRAD5A is a DNA translocase harboring a HIRAN domain which confers binding to branched DNA structures and is required for DNA repair in vivo.2016 · DOI: 10.1111/tpj.13283

Rice

No hit for this species in the current source table.

Functional annotation source
View annotation sources

Functional annotation source: OH1004 · LXL04_011047 · GCA_047496595.1_OSU_TarKok_2.0. These OH1004 annotations are retrieved through ID mapping; the Arabidopsis/rice table below uses protein alignments from the query reference.

GO annotations (OH1004 source)
GO:0006281 DNA repair Biological Process
GO:0006351 DNA-templated transcription Biological Process
GO:0080188 gene silencing by siRNA-directed DNA methylation Biological Process
GO:0005634 nucleus Cellular Component
GO:0003677 DNA binding Molecular Function
GO:0004386 helicase activity Molecular Function
GO:0005524 ATP binding Molecular Function
GO:0008094 ATP-dependent activity, acting on DNA Molecular Function
GO:0008270 zinc ion binding Molecular Function
GO:0016787 hydrolase activity Molecular Function
KEGG gene cross-reference
ath:AT1G50410
ath:AT3G20010
These KEGG gene identifiers are linked through homologous proteins; they do not establish pathway function for this gene.
Open Annotation Module

Gene expression

View expression in different studies, tissues and treatments. Results are presented separately by study and measurement unit.

View expression for this gene
Data sources and gene correspondence

Expression data come from public transcriptome studies. Reference genomes, sample metadata and measurement units are shown with the results. Ambiguous cross-reference correspondences do not select an expression record automatically; missing values do not mean zero expression.

Subcellular Localization Top 5

Computational predictions or homology annotations below do not replace localization experiments.

Nucleus0.939
Rank 1 · TkA03G561890 · TK1151
Cytoplasm0.103
Rank 2 · TkA03G561890 · TK1151
Cell membrane0.022
Rank 3 · TkA03G561890 · TK1151
Mitochondrion0.018
Rank 4 · TkA03G561890 · TK1151
Plastid0.014
Rank 5 · TkA03G561890 · TK1151

LocPro · Direct prediction · Computational prediction, not experimental localization

Open Subcellular Module

Predicted Functional Domains

Domain results are from Pfam-A/HMMER; positions are amino-acid coordinates on the protein sequence.

PF23048SH3-A_UBE2O41-65 aa
PF00176SNF2-rel_dom219-601 aa
PF00270DEAD219-474 aa
PF00271Helicase_C323-362 aa
PF20491Ermin385-444 aa
PF23048SH3-A_UBE2O386-434 aa
PF08158SDA1_HEAT387-434 aa
PF08158SDA1_HEAT496-529 aa
Gene IDDomain IDDomain NameStart aaEnd aaE-valueScore
TkA03G561890PF23048SH3-A_UBE2O41650.1113.9
TkA03G561890PF00176SNF2-rel_dom2196013.9e-73246.8
TkA03G561890PF00270DEAD2194740.002818.1
TkA03G561890PF00271Helicase_C3233621.7e-2074.0
TkA03G561890PF20491Ermin3854440.899.6
TkA03G561890PF23048SH3-A_UBE2O3864340.1113.9
TkA03G561890PF08158SDA1_HEAT3874343.97.1
TkA03G561890PF08158SDA1_HEAT4965293.97.1
TkA03G561890PF14835zf-RING_66346700.05214.2
TkA03G561890PF13920zf-C3HC4_36406782.5e-0524.7
TkA03G561890PF24921RING_XB3-XBAT316406730.01316.3
TkA03G561890PF00097zf-C3HC46416781.2e-0629.0
TkA03G561890PF13923zf-C3HC4_26416771.2e-0628.9
TkA03G561890PF14634zf-RING_56416780.0003621.1
TkA03G561890PF12678zf-rbx16416770.0006920.5
TkA03G561890PF14447Prok-RING_46416770.001319.3

Arabidopsis / Rice Protein Homology

Only Arabidopsis and rice are shown. Swiss-Prot entries are reviewed; TrEMBL entries are supplementary sequence candidates. Similarity is not experimental validation.

Download current result

ProteinOrganismDescriptionIdentityDatabaseConfidence
Q94BR5Arabidopsis thalianasp|Q94BR5|CHR28_ARATH Helicase-like transcription factor CHR2853.800%Swiss-ProtHigh
Q9LHE4Arabidopsis thalianasp|Q9LHE4|CHR27_ARATH Helicase-like transcription factor CHR2752.100%Swiss-ProtHigh
Q9FIY7Arabidopsis thalianasp|Q9FIY7|SM3L3_ARATH DNA repair protein RAD5B33.400%Swiss-ProtMedium
Q9FNI6Arabidopsis thalianasp|Q9FNI6|SM3L2_ARATH DNA repair protein RAD5A32.600%Swiss-ProtMedium

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